2Provincial Laboratory for Public Health (ProvLab), University of Alberta Hospital, Edmonton, Alberta, Canada.
‡Present address: Provincial Laboratory for Public Health, Edmonton, Canada.
Microb Genom. 2018 Jul;4(7). doi: 10.1099/mgen.0.000175. Epub 2018 Apr 9.
Distinuishing the species of mitis group streptococci is challenging due to ambiguous phenotypic characteristics and high degree of genetic similarity. This has been particularly true for resolving atypical Streptococcus pneumoniae and Streptococcus pseudopneumoniae. We used phylogenetic clustering to demonstrate specific and separate clades for both S. pneumoniae and S. pseudopneumoniae genomes. The genomes that clustered within these defined clades were used to extract species-specific genes from the pan-genome. The S. pneumoniae marker was detected in 8027 out of 8051 (>99.7 %) S. pneumoniae genomes. The S. pseudopneumoniae marker was specific for all genomes that clustered in the S. pseudopneumoniae clade, including unresolved species of the genus Streptococcus sequenced by the BC Centre for Disease Control Public Health Laboratory that previously could not be distinguished by other methods. Other than the presence of the S. pseudopneumoniae marker in six of 8051 (<0.08 %) S. pneumoniae genomes, both the S. pneumoniae and S. pseudopneumoniae markers showed little to no detectable cross-reactivity to the genomes of any other species of the genus Streptococcus or to a panel of over 46 000 genomes from viral, fungal, bacterial pathogens and microbiota commonly found in the respiratory tract. A real-time PCR assay was designed targeting these two markers. Genomics provides a useful technique for PCR assay design and development.
区分米蒂斯组链球菌的物种具有挑战性，因为其表型特征不明确且遗传相似度高。这对于解决非典型肺炎链球菌和假肺炎链球菌尤为如此。我们使用系统发育聚类来证明肺炎链球菌和假肺炎链球菌基因组都具有特定且独立的分支。聚类在这些定义的分支内的基因组用于从泛基因组中提取物种特异性基因。在 8051 个肺炎链球菌基因组中的 8027 个（>99.7%）中检测到肺炎链球菌标记。假肺炎链球菌标记特异性针对所有聚类在假肺炎链球菌分支内的基因组，包括以前无法通过其他方法区分的 BC 疾病控制中心公共卫生实验室测序的属链球菌未解决的种。除了在 8051 个肺炎链球菌基因组中的 6 个（<0.08%）中存在假肺炎链球菌标记外，肺炎链球菌和假肺炎链球菌标记与属链球菌的任何其他物种的基因组或呼吸道中常见的病毒、真菌、细菌病原体和微生物群落的超过 46000 个基因组的面板几乎没有或没有可检测的交叉反应性。设计了针对这两个标记的实时 PCR 检测。基因组学为 PCR 检测设计和开发提供了有用的技术。
